ENST00000648086.1:c.*875A>G

Variant names:

• chr6-169420286-T-C
• rs438465
• ENST00000648086.1:c.*875A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000648086.1(ENSG00000285733):​c.*875A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.819 in 152,004 control chromosomes in the GnomAD database, including 51,871 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.82 (51871 hom., cov: 30)
• Consequence: ENSG00000285733 ENST00000648086.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.460
• Publications: 6 publications found

Genes affected

ENSG00000285733 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.892 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000648086.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285733	ENST00000648086.1		c.*875A>G		3_prime_UTR	Exon 8 of 8	ENSP00000497979.1
	ENSG00000285887	ENST00000649318.1		n.2876A>G		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000285733	ENST00000650382.1		n.2014A>G		non_coding_transcript_exon	Exon 11 of 11

Frequencies

GnomAD3 genomes AF: 0.819 AC: 124388 AN: 151884 Hom.: 51825 Cov.: 30

Gnomad AFR AF: 0.899

Gnomad AMI AF: 0.877

Gnomad AMR AF: 0.697

Gnomad ASJ AF: 0.832

Gnomad EAS AF: 0.389

Gnomad SAS AF: 0.732

Gnomad FIN AF: 0.811

Gnomad MID AF: 0.835

Gnomad NFE AF: 0.836

Gnomad OTH AF: 0.821

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.819 AC: 124488 AN: 152004 Hom.: 51871 Cov.: 30 AF XY: 0.811 AC XY: 60240 AN XY: 74268

African (AFR) AF: 0.899 AC: 37316 AN: 41486

American (AMR) AF: 0.696 AC: 10631 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.832 AC: 2886 AN: 3468

East Asian (EAS) AF: 0.389 AC: 2001 AN: 5146

South Asian (SAS) AF: 0.730 AC: 3509 AN: 4804

European-Finnish (FIN) AF: 0.811 AC: 8538 AN: 10534

Middle Eastern (MID) AF: 0.830 AC: 244 AN: 294

European-Non Finnish (NFE) AF: 0.836 AC: 56826 AN: 67984

Other (OTH) AF: 0.823 AC: 1737 AN: 2110

Alfa AF: 0.816 Hom.: 30822

Bravo AF: 0.815

Asia WGS AF: 0.647 AC: 2254 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.69
DANN	Benign	0.34
PhyloP100		-0.46

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs438465; hg19: chr6-169820381;